## [1] "data/config.vertebrata_minimal.yaml"
Analysis report - 24 January, 2023 - 21:33 CET - version: 0.9.7
Location of genomes files:
results/assemblies
Total number of included genomes: 25
Locally provided genomes: 1
Successfully downloaded genomes: 24
Failed species downloads: 0
Not downloaded:
Information on successfully downloaded genomes:
info <- ""
if (file.exists(downloaded_genomes_statistics_file))
{
if (file.size(downloaded_genomes_statistics_file) != 0) {
data <- read.csv(downloaded_genomes_statistics_file, sep="\t", header=T)
} else {
info <- "*No information about downloaded genomes found. Maybe you only have local species?*"
}
data %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px") # %>% mutate(ftp_path = cell_spec("download", "html", link = ftp_path)) %>% kbl(escape=F) %>% kable_paper("hover", full_width = F) %>% scroll_box(width = "100%", height = "600px")
} else {
info <- "*No information about downloaded genomes found. Did you run phylociraptor setup ?*"
}
| name | id | assembly_accession | bioproject | biosample | wgs_master | refseq_category | taxid | species_taxid | organism_name | infraspecific_name | isolate | version_status | assembly_level | release_type | genome_rep | seq_rel_date | asm_name | submitter | gbrs_paired_asm | paired_asm_comp | ftp_path | excluded_from_refseq | relation_to_type_material | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Amblyraja_radiata | 529558 | GCA_010909765.2 | PRJNA591369 | SAMN09948523 | JAAGWR000000000.1 | representative genome | 386614 | 386614 | Amblyraja radiata | CabotCenter1 | latest | Chromosome | Minor | Full | 2020/02/21 | sAmbRad1.1.pri | Vertebrate Genomes Project | GCF_010909765.2 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/909/765/GCA_010909765.2_sAmbRad1.1.pri | NA | na | ||
| Anolis_carolinensis | 1121 | GCA_000090745.2 | PRJNA18787 | SAMN02981230 | AAWZ00000000.2 | representative genome | 28377 | 28377 | Anolis carolinensis | latest | Chromosome | Minor | Full | 2011/01/10 | AnoCar2.0 | Broad Institute | GCF_000090745.1 | identical | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/090/745/GCA_000090745.2_AnoCar2.0 | NA | na | |||
| Callorhinchus_milii | 2221 | GCA_000165045.2 | PRJNA18361 | SAMN00000800 | AAVX00000000.2 | na | 7868 | 7868 | Callorhinchus milii | IMCB2004 | latest | Scaffold | Major | Full | 2013/12/11 | Callorhinchus_milii-6.1.3 | Institute of Molecular and Cell Biology, Singapore | GCF_000165045.1 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/165/045/GCA_000165045.2_Callorhinchus_milii-6.1.3 | superseded by newer assembly for species | NA | na | |
| Canis_lupus | 1488310 | GCA_905319855.2 | PRJEB43200 | SAMEA7532739 | CAJNRB000000000.2 | na | 9612 | 9612 | Canis lupus | latest | Chromosome | Major | Full | 2021/03/26 | mCanLor1.2 | WELLCOME SANGER INSTITUTE | na | na | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/319/855/GCA_905319855.2_mCanLor1.2 | NA | na | |||
| Danio_kyathit | 1465680 | GCA_903798195.1 | PRJEB38580 | SAMEA104130240 | CAIGQS000000000.1 | representative genome | 242068 | 242068 | Danio kyathit | latest | Chromosome | Major | Full | 2020/06/27 | fDanKya3.1 | SC | na | na | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/798/195/GCA_903798195.1_fDanKya3.1 | NA | na | |||
| Dasypus_novemcinctus | 3904 | GCA_000208655.2 | PRJNA12594 | SAMN02953623 | na | na | 9361 | 9361 | Dasypus novemcinctus | 3-136 | replaced | Scaffold | Major | Full | na | na | Baylor College of Medicine | GCF_000208655.3 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/208/655/GCA_000208655.2_Dasnov3.0 | NA | na | ||
| Eptatretus_burgeri | 1396691 | GCA_900186335.2 | PRJEB21290 | SAMEA104124530 | FYBX00000000.2 | na | 7764 | 7764 | Eptatretus burgeri | latest | Scaffold | Major | Full | 2017/10/24 | Eburgeri_3.2 | RIKEN CENTER FOR DEVELOPMENTAL BIOLOGY | na | na | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/186/335/GCA_900186335.2_Eburgeri_3.2 | NA | na | |||
| Gallus_gallus | 815795 | GCA_016699485.1 | PRJNA660757 | SAMN15960293 | JAENSK000000000.1 | representative genome | 9031 | 9031 | Gallus gallus | breed=Cross of Broiler mother + white leghorn layer father | bGalGal1 | latest | Chromosome | Major | Full | 2021/01/19 | bGalGal1.mat.broiler.GRCg7b | Vertebrate Genomes Project | GCF_016699485.2 | identical | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/699/485/GCA_016699485.1_bGalGal1.mat.broiler.GRCg7b | NA | na | |
| Homo_sapiens | 1 | GCA_000001405.28 | PRJNA31257 | na | na | 9606 | 9606 | Homo sapiens | replaced | Chromosome | Patch | Full | na | na | Genome Reference Consortium | GCF_000001405.40 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13 | NA | na | ||||
| Latimeria_chalumnae | 4626 | GCA_000225785.1 | PRJNA56111 | SAMN00138723 | AFYH00000000.1 | representative genome | 7897 | 7897 | Latimeria chalumnae | SAIAB 97564 | latest | Scaffold | Major | Full | 2011/09/12 | LatCha1 | Broad Institute | GCF_000225785.1 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/225/785/GCA_000225785.1_LatCha1 | NA | na | ||
| Loxodonta_africana | 8 | GCA_000001905.1 | PRJNA12569 | SAMN02953622 | AAGU00000000.3 | representative genome | 9785 | 9785 | Loxodonta africana | ISIS603380 | latest | Scaffold | Major | Full | 2009/07/15 | Loxafr3.0 | Broad Institute | GCF_000001905.1 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/905/GCA_000001905.1_Loxafr3.0 | NA | na | ||
| Meleagris_gallopavo | 1361 | GCA_000146605.4 | PRJNA42129 | SAMN02981253 | ADDD00000000.2 | representative genome | 9103 | 9103 | Meleagris gallopavo | breed=Aviagen turkey brand Nicholas breeding stock | NT-WF06-2002-E0010 | latest | Chromosome | Minor | Full | 2019/10/21 | Turkey_5.1 | Turkey Genome Consortium | GCF_000146605.3 | identical | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/146/605/GCA_000146605.4_Turkey_5.1 | NA | na | |
| Monodelphis_domestica | 23 | GCA_000002295.1 | PRJNA12561 | SAMN02953611 | AAFR00000000.3 | representative genome | 13616 | 13616 | Monodelphis domestica | latest | Chromosome | Major | Full | 2007/01/25 | MonDom5 | The Genome Sequencing Platform, The Genome Assembly Team | GCF_000002295.2 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/295/GCA_000002295.1_MonDom5 | NA | na | |||
| Mus_musculus | 4 | GCA_000001635.9 | PRJNA20689 | reference genome | 10090 | 10090 | Mus musculus | strain=C57BL/6J | latest | Chromosome | Major | Full | 2020/06/24 | GRCm39 | Genome Reference Consortium | GCF_000001635.27 | identical | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39 | NA | na | ||||
| Neoceratodus_forsteri | 794647 | GCA_016271365.1 | PRJNA644903 | SAMN15471169 | JADMNL000000000.1 | representative genome | 7892 | 7892 | Neoceratodus forsteri | LF-2020 | latest | Chromosome | Major | Full | 2020/12/28 | neoFor_v3 | University of Konstanz | na | na | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/271/365/GCA_016271365.1_neoFor_v3 | NA | na | ||
| Notamacropus_eugenii | 75 | GCA_000004035.1 | PRJNA12587 | ABQO000000000.1 | representative genome | 9315 | 9315 | Notamacropus eugenii | latest | Scaffold | Major | Full | 2009/11/06 | Meug_1.1 | Tammar Wallaby Genome Sequencing Consortium | na | na | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/004/035/GCA_000004035.1_Meug_1.1 | NA | na | ||||
| Oreochromis_niloticus | 83287 | GCA_001858045.3 | PRJNA344471 | SAMN05859795 | MKQE00000000.2 | representative genome | 8128 | 8128 | Oreochromis niloticus | F11D_XX | latest | Chromosome | Major | Full | 2018/06/29 | O_niloticus_UMD_NMBU | University of Maryland | GCF_001858045.2 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/858/045/GCA_001858045.3_O_niloticus_UMD_NMBU | NA | na | ||
| Ornithorhynchus_anatinus | 194658 | GCA_004115215.4 | PRJNA489114 | SAMN08537700 | RZJT00000000.2 | representative genome | 9258 | 9258 | Ornithorhynchus anatinus | Pmale09 | latest | Chromosome | Major | Full | 2020/11/06 | mOrnAna1.pri.v4 | Vertebrate Genomes Project | GCF_004115215.2 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/115/215/GCA_004115215.4_mOrnAna1.pri.v4 | NA | na | ||
| Petromyzon_marinus | 533746 | GCA_010993605.1 | PRJNA562011 | SAMN12629506 | JAAIYE000000000.1 | representative genome | 7757 | 7757 | Petromyzon marinus | kPetMar1 | latest | Chromosome | Major | Full | 2020/02/24 | kPetMar1.pri | Vertebrate Genomes Project | GCF_010993605.1 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/010/993/605/GCA_010993605.1_kPetMar1.pri | NA | na | ||
| Rana_temporaria | 1484741 | GCA_905171775.1 | PRJEB42171 | SAMEA7521635 | CAJIMO000000000.1 | representative genome | 8407 | 8407 | Rana temporaria | latest | Chromosome | Major | Full | 2021/01/28 | aRanTem1.1 | Wellcome Sanger Institute | GCF_905171775.1 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/905/171/775/GCA_905171775.1_aRanTem1.1 | NA | na | |||
| Scyliorhinus_canicula | 1453583 | GCA_902713615.2 | PRJEB35945 | SAMEA994730 | CACTIT000000000.2 | representative genome | 7830 | 7830 | Scyliorhinus canicula | latest | Chromosome | Major | Full | 2021/01/28 | sScyCan1.2 | Wellcome Sanger Institute | na | na | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/713/615/GCA_902713615.2_sScyCan1.2 | NA | na | |||
| Taeniopygia_guttata | 428230 | GCA_008822105.2 | PRJNA555095 | SAMN09946140 | VOHI00000000.2 | na | 59729 | 59729 | Taeniopygia guttata | Blue55 | latest | Chromosome | Major | Full | 2020/02/21 | bTaeGut2.pat.W.v2 | Vertebrate Genomes Project | GCF_008822105.2 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/008/822/105/GCA_008822105.2_bTaeGut2.pat.W.v2 | superseded by newer assembly for species | NA | na | |
| Takifugu_rubripes | 1419030 | GCA_901000725.3 | PRJEB31988 | SAMEA104384834 | CAAJGN000000000.3 | representative genome | 31033 | 31033 | Takifugu rubripes | latest | Chromosome | Major | Full | 2021/04/24 | fTakRub1.3 | Wellcome Sanger Institute | na | na | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/901/000/725/GCA_901000725.3_fTakRub1.3 | NA | na | |||
| Xenopus_tropicalis | 80 | GCA_000004195.4 | PRJNA577946 | SAMN13041969 | AAMC00000000.4 | representative genome | 8364 | 8364 | Xenopus tropicalis | strain=Nigerian | latest | Chromosome | Major | Full | 2019/11/14 | UCB_Xtro_10.0 | University of California, Berkeley | GCF_000004195.4 | different | https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/004/195/GCA_000004195.4_UCB_Xtro_10.0 | NA | na |
Orthologous genes were inferred using BUSCO.
Location of BUSCO results:
results/orthology/busco
Used BUSCO set: vertebrata_odb10
Total number of BUSCO genes in BUSCO set: 20
Number of BUSCO genes recovered in too few (20) samples: 3
BUSCO genes below threshold:
228730at7742, 164538at7742, 320238at7742
Number of samples with single-copy BUSCO score below threshold (0.5): 0
Genomes below threshold:
| species | single_copy | duplicated | fragmented | missing |
|---|---|---|---|---|
| Amblyraja_radiata | 2999 | 71 | 98 | 186 |
| Anolis_carolinensis | 2861 | 22 | 169 | 302 |
| Callorhinchus_milii | 2976 | 34 | 131 | 213 |
| Canis_lupus | 3122 | 47 | 65 | 120 |
| Danio_kyathit | 3107 | 45 | 75 | 127 |
| Dasypus_novemcinctus | 2717 | 61 | 212 | 364 |
| Eptatretus_burgeri | 1612 | 59 | 490 | 1193 |
| Gallus_gallus | 3180 | 29 | 45 | 100 |
| Homo_sapiens | 2984 | 130 | 77 | 163 |
| Latimeria_chalumnae | 2795 | 30 | 279 | 250 |
| Loxodonta_africana | 3039 | 22 | 103 | 190 |
| Meleagris_gallopavo | 2872 | 19 | 205 | 258 |
| Monodelphis_domestica | 3049 | 142 | 76 | 87 |
| Mus_musculus | 3124 | 55 | 51 | 124 |
| Neoceratodus_forsteri | 2101 | 75 | 723 | 455 |
| Notamacropus_eugenii | 1169 | 29 | 514 | 1642 |
| Oreochromis_niloticus | 3275 | 20 | 25 | 34 |
| Ornithorhynchus_anatinus | 3075 | 36 | 141 | 102 |
| Petromyzon_marinus | 2275 | 59 | 193 | 827 |
| Protopterus_annectens | 2029 | 1130 | 105 | 90 |
| Rana_temporaria | 3088 | 74 | 76 | 116 |
| Scyliorhinus_canicula | 2977 | 102 | 106 | 169 |
| Taeniopygia_guttata | 3161 | 19 | 50 | 124 |
| Takifugu_rubripes | 3120 | 77 | 73 | 84 |
| Xenopus_tropicalis | 3231 | 34 | 30 | 59 |
Location of alignment files:
results/alignments/full
| length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 193525at7742_aligned.fas | 652 | 25 | 179 | 617 | 35 | 675 | 25 | 180 | 641 | 34 | 690 | 25 | 178 | 655 | 35 |
| 359032at7742_aligned.fas | 347 | 25 | 104 | 325 | 22 | 351 | 25 | 106 | 329 | 22 | 347 | 25 | 105 | 325 | 22 |
| 406935at7742_aligned.fas | 292 | 25 | 75 | 276 | 16 | 299 | 25 | 80 | 283 | 16 | 305 | 25 | 81 | 289 | 16 |
| 97645at7742_aligned.fas | 1237 | 24 | 290 | 1162 | 75 | 1310 | 24 | 287 | 1233 | 77 | 1399 | 24 | 291 | 1320 | 79 |
| 332227at7742_aligned.fas | 554 | 23 | 169 | 508 | 46 | 552 | 23 | 168 | 506 | 46 | 565 | 23 | 166 | 519 | 46 |
| 361842at7742_aligned.fas | 352 | 25 | 74 | 334 | 18 | 365 | 25 | 75 | 345 | 20 | 364 | 25 | 79 | 344 | 20 |
| 409625at7742_aligned.fas | 244 | 25 | 69 | 234 | 10 | 244 | 25 | 67 | 232 | 12 | 246 | 25 | 67 | 234 | 12 |
| 33940at7742_aligned.fas | 1351 | 25 | 102 | 1085 | 266 | 1394 | 25 | 111 | 1123 | 271 | 1397 | 25 | 103 | 1127 | 270 |
| 378120at7742_aligned.fas | 266 | 25 | 116 | 216 | 50 | 277 | 25 | 118 | 227 | 50 | 291 | 25 | 105 | 241 | 50 |
| 409719at7742_aligned.fas | 410 | 25 | 72 | 388 | 22 | 369 | 25 | 72 | 347 | 22 | 443 | 25 | 72 | 421 | 22 |
| 342641at7742_aligned.fas | 364 | 25 | 127 | 324 | 40 | 368 | 25 | 130 | 327 | 41 | 374 | 25 | 128 | 333 | 41 |
| 403632at7742_aligned.fas | 423 | 25 | 34 | 412 | 11 | 431 | 25 | 44 | 420 | 11 | 441 | 25 | 41 | 430 | 11 |
| 413149at7742_aligned.fas | 232 | 25 | 75 | 226 | 6 | 245 | 25 | 86 | 239 | 6 | 236 | 25 | 78 | 230 | 6 |
| 353318at7742_aligned.fas | 382 | 25 | 86 | 369 | 13 | 390 | 25 | 88 | 377 | 13 | 397 | 25 | 90 | 384 | 13 |
| 404316at7742_aligned.fas | 262 | 25 | 66 | 221 | 41 | 256 | 25 | 66 | 215 | 41 | 271 | 25 | 65 | 230 | 41 |
| 42971at7742_aligned.fas | 1327 | 23 | 448 | 1037 | 290 | 1351 | 23 | 462 | 1060 | 291 | 1372 | 23 | 464 | 1082 | 290 |
Location of trimmed alignment files:
results/alignments/trimmed
Parsimony informative sites cutoff: 50
| alignment | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 193525at7742_aligned_trimmed.fas | 448 | 25 | 178 | 404 | 44 | 454 | 25 | 179 | 419 | 35 | 461 | 25 | 179 | 417 | 44 | 469 | 25 | 180 | 435 | 34 | 470 | 25 | 176 | 426 | 44 | 469 | 25 | 178 | 434 | 35 |
| 332227at7742_aligned_trimmed.fas | 288 | 23 | 141 | 223 | 65 | 298 | 23 | 169 | 252 | 46 | 296 | 23 | 139 | 231 | 65 | 299 | 23 | 168 | 253 | 46 | 288 | 23 | 142 | 223 | 65 | 296 | 23 | 166 | 250 | 46 |
| 33940at7742_aligned_trimmed.fas | 1114 | 25 | 101 | 801 | 313 | 1018 | 25 | 102 | 752 | 266 | 1129 | 25 | 110 | 808 | 321 | 1022 | 25 | 111 | 751 | 271 | 1105 | 25 | 102 | 786 | 319 | 1016 | 25 | 103 | 746 | 270 |
| 342641at7742_aligned_trimmed.fas | 275 | 25 | 119 | 233 | 42 | 259 | 25 | 127 | 219 | 40 | 282 | 25 | 122 | 240 | 42 | 264 | 25 | 130 | 223 | 41 | 292 | 25 | 122 | 250 | 42 | 265 | 25 | 128 | 224 | 41 |
| 353318at7742_aligned_trimmed.fas | 206 | 25 | 87 | 193 | 13 | 214 | 25 | 86 | 201 | 13 | 205 | 25 | 89 | 192 | 13 | 232 | 25 | 88 | 219 | 13 | 205 | 25 | 91 | 192 | 13 | 250 | 25 | 90 | 237 | 13 |
| 359032at7742_aligned_trimmed.fas | 166 | 25 | 104 | 142 | 24 | 254 | 25 | 104 | 232 | 22 | 166 | 25 | 104 | 142 | 24 | 239 | 25 | 106 | 217 | 22 | 165 | 25 | 103 | 141 | 24 | 191 | 25 | 105 | 169 | 22 |
| 361842at7742_aligned_trimmed.fas | 233 | 25 | 75 | 212 | 21 | 219 | 25 | 74 | 201 | 18 | 239 | 25 | 76 | 215 | 24 | 219 | 25 | 75 | 199 | 20 | 235 | 25 | 77 | 211 | 24 | 218 | 25 | 79 | 198 | 20 |
| 378120at7742_aligned_trimmed.fas | 253 | 25 | 115 | 192 | 61 | 253 | 25 | 116 | 203 | 50 | 261 | 25 | 117 | 200 | 61 | 253 | 25 | 118 | 203 | 50 | 257 | 25 | 104 | 196 | 61 | 252 | 25 | 105 | 202 | 50 |
| 403632at7742_aligned_trimmed.fas | 176 | 25 | 31 | 161 | 15 | 166 | 25 | 34 | 155 | 11 | 190 | 25 | 41 | 175 | 15 | 171 | 25 | 44 | 160 | 11 | 192 | 25 | 41 | 177 | 15 | 171 | 25 | 41 | 160 | 11 |
| 404316at7742_aligned_trimmed.fas | 204 | 25 | 67 | 158 | 46 | 217 | 25 | 66 | 176 | 41 | 207 | 25 | 67 | 161 | 46 | 219 | 25 | 66 | 178 | 41 | 205 | 25 | 66 | 159 | 46 | 217 | 25 | 65 | 176 | 41 |
| 406935at7742_aligned_trimmed.fas | 139 | 25 | 75 | 119 | 20 | 204 | 25 | 75 | 188 | 16 | 147 | 25 | 80 | 125 | 22 | 207 | 25 | 80 | 191 | 16 | 142 | 25 | 81 | 120 | 22 | 206 | 25 | 81 | 190 | 16 |
| 409625at7742_aligned_trimmed.fas | 132 | 25 | 69 | 120 | 12 | 137 | 25 | 69 | 127 | 10 | 139 | 25 | 67 | 125 | 14 | 134 | 25 | 67 | 122 | 12 | 138 | 25 | 67 | 124 | 14 | 133 | 25 | 67 | 121 | 12 |
| 409719at7742_aligned_trimmed.fas | 131 | 25 | 72 | 108 | 23 | 227 | 25 | 72 | 205 | 22 | 134 | 25 | 72 | 111 | 23 | 151 | 25 | 72 | 129 | 22 | 130 | 25 | 72 | 107 | 23 | 228 | 25 | 72 | 206 | 22 |
| 413149at7742_aligned_trimmed.fas | 104 | 25 | 67 | 95 | 9 | 124 | 25 | 75 | 118 | 6 | 112 | 25 | 72 | 103 | 9 | 125 | 25 | 86 | 119 | 6 | 106 | 25 | 67 | 97 | 9 | 127 | 25 | 78 | 121 | 6 |
| 42971at7742_aligned_trimmed.fas | 935 | 23 | 413 | 625 | 310 | 1016 | 23 | 448 | 726 | 290 | 943 | 23 | 415 | 632 | 311 | 998 | 23 | 462 | 707 | 291 | 926 | 23 | 415 | 616 | 310 | 1026 | 23 | 464 | 736 | 290 |
| 97645at7742_aligned_trimmed.fas | 798 | 24 | 284 | 705 | 93 | 747 | 24 | 290 | 672 | 75 | 822 | 24 | 279 | 725 | 97 | 736 | 24 | 287 | 659 | 77 | 837 | 24 | 280 | 739 | 98 | 740 | 24 | 291 | 661 | 79 |
Location of filtered alignment files:
results/alignments/filtered
Parsimony informative sites cutoff: 50
| alignment | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed | length | nseqs | nparsimony | nvariable | nfixed |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 193525at7742_aligned_trimmed.fas | 448 | 25 | 178 | 404 | 44 | 454 | 25 | 179 | 419 | 35 | 461 | 25 | 179 | 417 | 44 | 469 | 25 | 180 | 435 | 34 | 470 | 25 | 176 | 426 | 44 | 469 | 25 | 178 | 434 | 35 |
| 332227at7742_aligned_trimmed.fas | 288 | 23 | 141 | 223 | 65 | 298 | 23 | 169 | 252 | 46 | 296 | 23 | 139 | 231 | 65 | 299 | 23 | 168 | 253 | 46 | 288 | 23 | 142 | 223 | 65 | 296 | 23 | 166 | 250 | 46 |
| 33940at7742_aligned_trimmed.fas | 1114 | 25 | 101 | 801 | 313 | 1018 | 25 | 102 | 752 | 266 | 1129 | 25 | 110 | 808 | 321 | 1022 | 25 | 111 | 751 | 271 | 1105 | 25 | 102 | 786 | 319 | 1016 | 25 | 103 | 746 | 270 |
| 342641at7742_aligned_trimmed.fas | 275 | 25 | 119 | 233 | 42 | 259 | 25 | 127 | 219 | 40 | 282 | 25 | 122 | 240 | 42 | 264 | 25 | 130 | 223 | 41 | 292 | 25 | 122 | 250 | 42 | 265 | 25 | 128 | 224 | 41 |
| 353318at7742_aligned_trimmed.fas | 206 | 25 | 87 | 193 | 13 | 214 | 25 | 86 | 201 | 13 | 205 | 25 | 89 | 192 | 13 | 232 | 25 | 88 | 219 | 13 | 205 | 25 | 91 | 192 | 13 | 250 | 25 | 90 | 237 | 13 |
| 359032at7742_aligned_trimmed.fas | 166 | 25 | 104 | 142 | 24 | 254 | 25 | 104 | 232 | 22 | 166 | 25 | 104 | 142 | 24 | 239 | 25 | 106 | 217 | 22 | 165 | 25 | 103 | 141 | 24 | 191 | 25 | 105 | 169 | 22 |
| 361842at7742_aligned_trimmed.fas | 233 | 25 | 75 | 212 | 21 | 219 | 25 | 74 | 201 | 18 | 239 | 25 | 76 | 215 | 24 | 219 | 25 | 75 | 199 | 20 | 235 | 25 | 77 | 211 | 24 | 218 | 25 | 79 | 198 | 20 |
| 378120at7742_aligned_trimmed.fas | 253 | 25 | 115 | 192 | 61 | 253 | 25 | 116 | 203 | 50 | 261 | 25 | 117 | 200 | 61 | 253 | 25 | 118 | 203 | 50 | 257 | 25 | 104 | 196 | 61 | 252 | 25 | 105 | 202 | 50 |
| 404316at7742_aligned_trimmed.fas | 204 | 25 | 67 | 158 | 46 | 217 | 25 | 66 | 176 | 41 | 207 | 25 | 67 | 161 | 46 | 219 | 25 | 66 | 178 | 41 | 205 | 25 | 66 | 159 | 46 | 217 | 25 | 65 | 176 | 41 |
| 406935at7742_aligned_trimmed.fas | 139 | 25 | 75 | 119 | 20 | 204 | 25 | 75 | 188 | 16 | 147 | 25 | 80 | 125 | 22 | 207 | 25 | 80 | 191 | 16 | 142 | 25 | 81 | 120 | 22 | 206 | 25 | 81 | 190 | 16 |
| 409625at7742_aligned_trimmed.fas | 132 | 25 | 69 | 120 | 12 | 137 | 25 | 69 | 127 | 10 | 139 | 25 | 67 | 125 | 14 | 134 | 25 | 67 | 122 | 12 | 138 | 25 | 67 | 124 | 14 | 133 | 25 | 67 | 121 | 12 |
| 409719at7742_aligned_trimmed.fas | 131 | 25 | 72 | 108 | 23 | 227 | 25 | 72 | 205 | 22 | 134 | 25 | 72 | 111 | 23 | 151 | 25 | 72 | 129 | 22 | 130 | 25 | 72 | 107 | 23 | 228 | 25 | 72 | 206 | 22 |
| 413149at7742_aligned_trimmed.fas | 104 | 25 | 67 | 95 | 9 | 124 | 25 | 75 | 118 | 6 | 112 | 25 | 72 | 103 | 9 | 125 | 25 | 86 | 119 | 6 | 106 | 25 | 67 | 97 | 9 | 127 | 25 | 78 | 121 | 6 |
| 42971at7742_aligned_trimmed.fas | 935 | 23 | 413 | 625 | 310 | 1016 | 23 | 448 | 726 | 290 | 943 | 23 | 415 | 632 | 311 | 998 | 23 | 462 | 707 | 291 | 926 | 23 | 415 | 616 | 310 | 1026 | 23 | 464 | 736 | 290 |
| 97645at7742_aligned_trimmed.fas | 798 | 24 | 284 | 705 | 93 | 747 | 24 | 290 | 672 | 75 | 822 | 24 | 279 | 725 | 97 | 736 | 24 | 287 | 659 | 77 | 837 | 24 | 280 | 739 | 98 | 740 | 24 | 291 | 661 | 79 |
Location of modeltesting files:
results/modeltest
Overview of individual modeltest results:
| alignment | clustalo-aliscore | clustalo-trimal | mafft-aliscore | mafft-trimal | muscle-aliscore | muscle-trimal |
|---|---|---|---|---|---|---|
| 193525at7742 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 |
| 332227at7742 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 |
| 33940at7742 | VT+R2 | VT+R2 | JTT+R2 | JTT+R2 | JTT+R2 | JTT+R2 |
| 342641at7742 | LG+I+G4 | LG+I+G4 | LG+I+G4 | LG+I+G4 | LG+I+G4 | LG+I+G4 |
| 353318at7742 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 | JTT+G4 |
| 359032at7742 | LG+G4 | JTT+I+G4 | LG+G4 | JTT+G4 | LG+G4 | JTT+G4 |
| 361842at7742 | LG+G4 | JTTDCMut+G4 | LG+G4 | JTTDCMut+G4 | JTTDCMut+G4 | JTTDCMut+G4 |
| 378120at7742 | JTTDCMut+F+G4 | JTTDCMut+F+R3 | LG+G4 | JTTDCMut+F+R3 | LG+G4 | LG+G4 |
| 404316at7742 | JTT+R2 | JTT+R3 | JTT+R2 | JTT+R3 | JTT+R2 | JTT+R3 |
| 406935at7742 | LG+G4 | VT+G4 | LG+G4 | LG+G4 | LG+G4 | VT+G4 |
| 409625at7742 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 |
| 409719at7742 | LG+G4 | JTT+I+G4 | LG+G4 | JTTDCMut+G4 | LG+G4 | JTT+I+G4 |
| 413149at7742 | JTTDCMut+G4 | JTTDCMut+G4 | JTTDCMut+G4 | JTTDCMut+G4 | WAG+G4 | JTTDCMut+G4 |
| 42971at7742 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 | JTT+I+G4 |
| 97645at7742 | JTT+R3 | JTT+R3 | JTT+R3 | JTT+R3 | JTT+R3 | JTT+R3 |
Location of gene trees:
results/modeltest
| gene | clustalo-aliscore | clustalo-trimal | mafft-aliscore | mafft-trimal | muscle-aliscore | muscle-trimal |
|---|---|---|---|---|---|---|
| 193525at7742 | 85 | 87 | 85 | 87 | 85 | 87 |
| 332227at7742 | 84 | 87 | 82 | 85 | 76 | 85 |
| 33940at7742 | 81 | 83 | 84 | 84 | 80 | 80 |
| 342641at7742 | 78 | 76 | 77 | 77 | 78 | 77 |
| 353318at7742 | 81 | 82 | 80 | 81 | 79 | 84 |
| 359032at7742 | 79 | 79 | 78 | 79 | 79 | 80 |
| 361842at7742 | 81 | 79 | 78 | 78 | 77 | 78 |
| 378120at7742 | 77 | 73 | 77 | 73 | 78 | 77 |
| 404316at7742 | 79 | 81 | 82 | 85 | 76 | 79 |
| 406935at7742 | 68 | 74 | 68 | 79 | 75 | 78 |
| 409625at7742 | 73 | 74 | 81 | 85 | 79 | 82 |
| 409719at7742 | 68 | 78 | 68 | 73 | 66 | 73 |
| 413149at7742 | 74 | 78 | 78 | 79 | 81 | 79 |
| 42971at7742 | 86 | 86 | 84 | 86 | 85 | 88 |
| 97645at7742 | 84 | 85 | 83 | 83 | 83 | 84 |
Location of phylogenetic results:
results/phylogeny-*/
| software | aligner | trimmer | boostraps | bootstrap-cutoff | ngenes | tree |
|---|---|---|---|---|---|---|
| iqtree | clustalo | aliscore | 1000 | 0 | 15 | |
| iqtree | clustalo | aliscore | 1000 | 50 | 15 | |
| iqtree | clustalo | aliscore | 1000 | 60 | 15 | |
| iqtree | clustalo | aliscore | 1000 | 70 | 13 | |
| iqtree | clustalo | aliscore | 1000 | 80 | 7 | |
| iqtree | clustalo | trimal | 1000 | 0 | 15 | |
| iqtree | clustalo | trimal | 1000 | 50 | 15 | |
| iqtree | clustalo | trimal | 1000 | 60 | 15 | |
| iqtree | clustalo | trimal | 1000 | 70 | 15 | |
| iqtree | clustalo | trimal | 1000 | 80 | 7 | |
| iqtree | mafft | aliscore | 1000 | 0 | 15 | |
| iqtree | mafft | aliscore | 1000 | 50 | 15 | |
| iqtree | mafft | aliscore | 1000 | 60 | 15 | |
| iqtree | mafft | aliscore | 1000 | 70 | 13 | |
| iqtree | mafft | aliscore | 1000 | 80 | 8 | |
| iqtree | mafft | trimal | 1000 | 0 | 15 | |
| iqtree | mafft | trimal | 1000 | 50 | 15 | |
| iqtree | mafft | trimal | 1000 | 60 | 15 | |
| iqtree | mafft | trimal | 1000 | 70 | 15 | |
| iqtree | mafft | trimal | 1000 | 80 | 8 | |
| iqtree | muscle | aliscore | 1000 | 0 | 15 | |
| iqtree | muscle | aliscore | 1000 | 50 | 15 | |
| iqtree | muscle | aliscore | 1000 | 60 | 15 | |
| iqtree | muscle | aliscore | 1000 | 70 | 14 | |
| iqtree | muscle | aliscore | 1000 | 80 | 5 | |
| iqtree | muscle | trimal | 1000 | 0 | 15 | |
| iqtree | muscle | trimal | 1000 | 50 | 15 | |
| iqtree | muscle | trimal | 1000 | 60 | 15 | |
| iqtree | muscle | trimal | 1000 | 70 | 15 | |
| iqtree | muscle | trimal | 1000 | 80 | 8 | |
| raxmlng | clustalo | aliscore | 100 | 0 | 15 | |
| raxmlng | clustalo | aliscore | 100 | 50 | 15 | |
| raxmlng | clustalo | aliscore | 100 | 60 | 15 | |
| raxmlng | clustalo | aliscore | 100 | 70 | 13 | |
| raxmlng | clustalo | aliscore | 100 | 80 | 7 | |
| raxmlng | clustalo | trimal | 100 | 0 | 15 | |
| raxmlng | clustalo | trimal | 100 | 50 | 15 | |
| raxmlng | clustalo | trimal | 100 | 60 | 15 | |
| raxmlng | clustalo | trimal | 100 | 70 | 15 | |
| raxmlng | clustalo | trimal | 100 | 80 | 7 | |
| raxmlng | mafft | aliscore | 100 | 0 | 15 | |
| raxmlng | mafft | aliscore | 100 | 50 | 15 | |
| raxmlng | mafft | aliscore | 100 | 60 | 15 | |
| raxmlng | mafft | aliscore | 100 | 70 | 13 | |
| raxmlng | mafft | aliscore | 100 | 80 | 8 | |
| raxmlng | mafft | trimal | 100 | 0 | 15 | |
| raxmlng | mafft | trimal | 100 | 50 | 15 | |
| raxmlng | mafft | trimal | 100 | 60 | 15 | |
| raxmlng | mafft | trimal | 100 | 70 | 15 | |
| raxmlng | mafft | trimal | 100 | 80 | 8 | |
| raxmlng | muscle | aliscore | 100 | 0 | 15 | |
| raxmlng | muscle | aliscore | 100 | 50 | 15 | |
| raxmlng | muscle | aliscore | 100 | 60 | 15 | |
| raxmlng | muscle | aliscore | 100 | 70 | 14 | |
| raxmlng | muscle | aliscore | 100 | 80 | 5 | |
| raxmlng | muscle | trimal | 100 | 0 | 15 | |
| raxmlng | muscle | trimal | 100 | 50 | 15 | |
| raxmlng | muscle | trimal | 100 | 60 | 15 | |
| raxmlng | muscle | trimal | 100 | 70 | 15 | |
| raxmlng | muscle | trimal | 100 | 80 | 8 |
Location of phylogenetic results:
results/phylogeny-*/
| software | aligner | trimmer | bootstrap-cutoff | ngenes | tree |
|---|---|---|---|---|---|
| astral | clustalo | aliscore | 0 | 15 | |
| astral | clustalo | aliscore | 50 | 15 | |
| astral | clustalo | aliscore | 60 | 15 | |
| astral | clustalo | aliscore | 70 | 13 | |
| astral | clustalo | aliscore | 80 | 7 | |
| astral | clustalo | trimal | 0 | 15 | |
| astral | clustalo | trimal | 50 | 15 | |
| astral | clustalo | trimal | 60 | 15 | |
| astral | clustalo | trimal | 70 | 15 | |
| astral | clustalo | trimal | 80 | 7 | |
| astral | mafft | aliscore | 0 | 15 | |
| astral | mafft | aliscore | 50 | 15 | |
| astral | mafft | aliscore | 60 | 15 | |
| astral | mafft | aliscore | 70 | 13 | |
| astral | mafft | aliscore | 80 | 8 | |
| astral | mafft | trimal | 0 | 15 | |
| astral | mafft | trimal | 50 | 15 | |
| astral | mafft | trimal | 60 | 15 | |
| astral | mafft | trimal | 70 | 15 | |
| astral | mafft | trimal | 80 | 8 | |
| astral | muscle | aliscore | 0 | 15 | |
| astral | muscle | aliscore | 50 | 15 | |
| astral | muscle | aliscore | 60 | 15 | |
| astral | muscle | aliscore | 70 | 14 | |
| astral | muscle | aliscore | 80 | 5 | |
| astral | muscle | trimal | 0 | 15 | |
| astral | muscle | trimal | 50 | 15 | |
| astral | muscle | trimal | 60 | 15 | |
| astral | muscle | trimal | 70 | 15 | |
| astral | muscle | trimal | 80 | 8 |
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 2
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 3
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 4
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 5
## Sun Jan 22 20:27:17 CET 2023 - Setup: Will download species now - batch: 1
## Sun Jan 22 20:36:51 CET 2023 - phylociraptor setup done.
## Mon Jan 23 10:02:55 CET 2023 - Pipeline part 1 (orthology) done.
## Mon Jan 23 10:03:29 CET 2023 - BUSCO files will be filtered on a per-sample basis. This could lower the number of species in the final tree.
## Mon Jan 23 10:03:32 CET 2023 - Number of BUSCO sequence files: 16
## Mon Jan 23 10:03:32 CET 2023 - Number of deduplicated BUSCO sequence files: 16
## Mon Jan 23 10:03:32 CET 2023 - Pipeline part filter-orthology done.
## Mon Jan 23 10:04:35 CET 2023 - Pipeline part 2 (align) done.
## Mon Jan 23 10:04:51 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:51 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:52 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:53 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:53 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:56 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:56 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 10:04:57 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:58 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 10:04:59 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:59 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 10:04:59 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:04:59 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:00 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:00 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:00 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:05:00 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:01 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:02 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:03 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:03 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:05 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:05 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 10:05:08 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:09 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:10 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:11 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:12 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 10:05:13 CET 2023 - Number of alignments (muscle): 16
## Mon Jan 23 10:05:13 CET 2023 - Number of trimmed alignments (muscle - trimal): 16
## Mon Jan 23 10:05:13 CET 2023 - Number of alignments (muscle - trimal) after filtering: 15
## Mon Jan 23 10:05:17 CET 2023 - Number of alignments (mafft): 16
## Mon Jan 23 10:05:17 CET 2023 - Number of trimmed alignments (mafft - trimal): 16
## Mon Jan 23 10:05:18 CET 2023 - Number of alignments (mafft - trimal) after filtering: 15
## Mon Jan 23 10:05:19 CET 2023 - Number of alignments (clustalo): 16
## Mon Jan 23 10:05:19 CET 2023 - Number of trimmed alignments (clustalo - trimal): 16
## Mon Jan 23 10:05:19 CET 2023 - Number of alignments (clustalo - trimal) after filtering: 15
## Mon Jan 23 10:05:22 CET 2023 - Number of alignments (muscle): 16
## Mon Jan 23 10:05:22 CET 2023 - Number of trimmed alignments (muscle - aliscore): 16
## Mon Jan 23 10:05:22 CET 2023 - Number of alignments (muscle - aliscore) after filtering: 15
## Mon Jan 23 10:05:27 CET 2023 - Number of alignments (mafft): 16
## Mon Jan 23 10:05:27 CET 2023 - Number of trimmed alignments (mafft - aliscore): 16
## Mon Jan 23 10:05:27 CET 2023 - Number of alignments (mafft - aliscore) after filtering: 15
## Mon Jan 23 10:05:27 CET 2023 - Number of alignments (clustalo): 16
## Mon Jan 23 10:05:27 CET 2023 - Number of trimmed alignments (clustalo - aliscore): 16
## Mon Jan 23 10:05:27 CET 2023 - Number of alignments (clustalo - aliscore) after filtering: 15
## Mon Jan 23 10:05:32 CET 2023 - Pipeline part filter_align done.
## Mon Jan 23 10:15:03 CET 2023 - Pipeline part modeltest (model) done.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:36 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:37 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:38 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 10:25:53 CET 2023 - Speciestree reconstruction done.
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:29 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:30 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:30 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:30 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:31 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:32 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:32 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:32 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:32 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:33 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 10:26:33 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 10:26:33 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:33 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:34 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 10:26:35 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:36 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:36 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:26:36 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 10:47:57 CET 2023 - Pipeline part 3 (tree) done.
## Mon Jan 23 11:11:45 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:45 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:46 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:51 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:51 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:52 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:52 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:52 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:53 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 11:11:55 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:56 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:57 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:58 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 11:11:59 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 20:26:40 CET 2023 - Setup: Will download species now - batch: 4
## Mon Jan 23 20:26:40 CET 2023 - Setup: Will download species now - batch: 3
## Mon Jan 23 20:29:15 CET 2023 - Setup: Will download species now - batch: 5
## Mon Jan 23 20:31:04 CET 2023 - Setup: Will download species now - batch: 2
## Mon Jan 23 20:33:50 CET 2023 - Setup: Will download species now - batch: 1
## Mon Jan 23 21:16:42 CET 2023 - phylociraptor setup done.
## Mon Jan 23 21:25:22 CET 2023 - Pipeline part 1 (orthology) done.
## Mon Jan 23 21:31:37 CET 2023 - Pipeline part 1 (orthology) done.
## Mon Jan 23 21:32:30 CET 2023 - Pipeline part filter-orthology done.
## Mon Jan 23 22:03:55 CET 2023 - Pipeline part filter-orthology done.
## Mon Jan 23 22:06:03 CET 2023 - Pipeline part 2 (align) done.
## Mon Jan 23 22:06:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:21 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:21 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:22 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:22 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:23 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:23 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:23 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:23 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:24 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:24 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:24 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:24 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:25 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:26 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:26 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:26 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:27 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:27 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:27 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:27 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 332227at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 42971at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 193525at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 33940at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 353318at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:28 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 97645at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:29 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:30 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 403632at7742
## Mon Jan 23 22:06:31 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:31 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:33 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:34 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409719at7742
## Mon Jan 23 22:06:34 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:35 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:35 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:35 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:36 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:36 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:36 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:36 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 342641at7742
## Mon Jan 23 22:06:44 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:44 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:44 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 361842at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:45 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 359032at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 378120at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:49 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 406935at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 409625at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 404316at7742
## Mon Jan 23 22:06:50 CET 2023 - The aliscore output file does not exist. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:51 CET 2023 - The aliscore output appears to be empty. Check results for BUSCO: 413149at7742
## Mon Jan 23 22:06:51 CET 2023 - Number of alignments (mafft): 16
## Mon Jan 23 22:06:51 CET 2023 - Number of trimmed alignments (mafft - trimal): 16
## Mon Jan 23 22:06:51 CET 2023 - Number of alignments (mafft - trimal) after filtering: 15
## Mon Jan 23 22:06:53 CET 2023 - Number of alignments (clustalo): 16
## Mon Jan 23 22:06:53 CET 2023 - Number of trimmed alignments (clustalo - trimal): 16
## Mon Jan 23 22:06:53 CET 2023 - Number of alignments (clustalo - trimal) after filtering: 15
## Mon Jan 23 22:06:59 CET 2023 - Number of alignments (muscle): 16
## Mon Jan 23 22:06:59 CET 2023 - Number of trimmed alignments (muscle - trimal): 16
## Mon Jan 23 22:06:59 CET 2023 - Number of alignments (muscle - trimal) after filtering: 15
## Mon Jan 23 22:07:04 CET 2023 - Number of alignments (clustalo): 16
## Mon Jan 23 22:07:04 CET 2023 - Number of trimmed alignments (clustalo - aliscore): 16
## Mon Jan 23 22:07:04 CET 2023 - Number of alignments (clustalo - aliscore) after filtering: 15
## Mon Jan 23 22:07:05 CET 2023 - Number of alignments (mafft): 16
## Mon Jan 23 22:07:05 CET 2023 - Number of trimmed alignments (mafft - aliscore): 16
## Mon Jan 23 22:07:05 CET 2023 - Number of alignments (mafft - aliscore) after filtering: 15
## Mon Jan 23 22:07:07 CET 2023 - Number of alignments (muscle): 16
## Mon Jan 23 22:07:07 CET 2023 - Number of trimmed alignments (muscle - aliscore): 16
## Mon Jan 23 22:07:07 CET 2023 - Number of alignments (muscle - aliscore) after filtering: 15
## Mon Jan 23 22:07:15 CET 2023 - Pipeline part filter_align done.
## Mon Jan 23 22:17:01 CET 2023 - Pipeline part modeltest (model) done.
## Mon Jan 23 22:24:46 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:46 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:46 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:47 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:48 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 0.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 70.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 50.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 60.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:24:49 CET 2023 - phylociraptor will use gene tree filtering based on average bootstrap support value of 80.
## Mon Jan 23 22:25:08 CET 2023 - Speciestree reconstruction done.
## Mon Jan 23 22:25:50 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 22:25:51 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:51 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:51 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:52 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 22:25:52 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 22:25:52 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 22:25:52 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:54 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:54 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:55 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:56 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:57 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 22:25:57 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 22:25:58 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:25:58 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:58 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (80) before creating concatenated alignment
## Mon Jan 23 22:25:58 CET 2023 - prepare_iqtree muscle-trimal: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 22:25:58 CET 2023 - prepare_iqtree mafft-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Mon Jan 23 22:25:59 CET 2023 - prepare_iqtree clustalo-aliscore: Will use bootstrap cutoff (50) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:59 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:25:59 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (80) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:00 CET 2023 - prepare_iqtree muscle-aliscore: Will use bootstrap cutoff (70) before creating concatenated alignment
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:00 CET 2023 - prepare_iqtree mafft-trimal: Will use bootstrap cutoff (60) before creating concatenated alignment
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:00 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (0) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:01 CET 2023 - prepare_iqtree clustalo-trimal: Will use bootstrap cutoff (70) before creating concatenated alignment
## Will create NEXUS partition file with model information now.
## Mon Jan 23 22:26:02 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:26:02 CET 2023 - nexus file for iqtree written.
## Mon Jan 23 22:38:26 CET 2023 - Pipeline part 3 (tree) done.
## Mon Jan 23 22:40:59 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:40:59 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:00 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:00 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:03 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:03 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:03 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:03 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 0 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 70 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate clustalo-trimal: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate clustalo-aliscore: Will use bootstrap cutoff 50 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-trimal: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate mafft-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-trimal: Will use bootstrap cutoff 60 before creating concatenated alignment
## Mon Jan 23 22:41:04 CET 2023 - concatenate muscle-aliscore: Will use bootstrap cutoff 80 before creating concatenated alignment
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:08 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:09 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:09 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:10 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Mon Jan 23 22:41:11 CET 2023 - 'phylociraptor model' finished successfully before. Will run raxml with best models.
## Tue Jan 24 21:05:06 CET 2023 - Pipeline part 3 (tree) done.
## Tue Jan 24 21:33:00 CET 2023 - Pipeline part ntree (njtree) done.